Biofloc technology (BFT) is one of the most sustainable aquaculture system, which is based on the principle of nutrient recycling and addition of carbon to enable heterotrophic microorganisms to the system. To evaluate the performance of the biofloc culture system for Cyprinus carpio fingerlings, a 60-day growth trial was conducted. The fingerlings (n = 600) of average body weight (4.92 g ± 0.14) were stocked in 12 circular fiberglass tanks (300 L, volume 10.59 cft) to form three biofloc treatments (T1, T2, and T3) along with one control group. The carbon sources for treatments were sugarcane molasses, tapioca, and wheat. The C/N ratio of 15 was maintained for all treatments. After 60 days of rearing, the fish were challenged with Aeromonas hydrophila, and the relative percentage survival (RPS) was observed over 14 days. A haematological, nonspecific immune, and stress parameters were analyzed using blood and serum samples collected at intervals of 20, 40, and 60 days. According to the results, the carbon sources affected the water quality parameters but were still adequate for fish welfare. An increased biofloc volume was observed with tapioca. Growth performance and better feed conversion ratio were recorded in biofloc with the tapioca group. The hematological parameters, including haemoglobin (Hb), hematocrit (HCT), white blood cells and lymphocytes were significantly (P <0.05) higher in biofloc-based tapioca group than in other treatments and control. Further, the serum protein, globulin, albumin, total immunoglobulin, and respiratory burst activity were also found significantly (P <0.05) higher in biofloc with tapioca as carbon source. However, the lysozyme activity was higher in biofloc with the wheat group. The RPS in tapioca was significantly higher, followed by biofloc with wheat. In conclusion, the tapioca-based biofloc can improve C. carpio growth, haematology, and nonspecific immune response under zero water exchange.